3L6R | pdb_00003l6r

The structure of mammalian serine racemase: Evidence for conformational changes upon inhibitor binding

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	PEG 3350, 200mM sodium malonate, 50mM MnCl2, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.543	α = 90
b = 84.212	β = 90
c = 70.376	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2008-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.98000	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	45.78	97.1	0.094	0.097	16.1	12.45	35305	35305	2	2	18.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	78.9		0.28	0.31	4.5	5.44

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.7	45.78	33537	1775	97.06	0.1676	0.15	0.202	0.2	RANDOM	23.399

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.02					0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.268
r_dihedral_angle_4_deg	15.399
r_dihedral_angle_3_deg	14.707
r_scangle_it	7.284
r_dihedral_angle_1_deg	5.75
r_scbond_it	4.755
r_mcangle_it	3.273
r_rigid_bond_restr	2.589
r_mcbond_it	2.073
r_angle_refined_deg	2.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.268
r_dihedral_angle_4_deg	15.399
r_dihedral_angle_3_deg	14.707
r_scangle_it	7.284
r_dihedral_angle_1_deg	5.75
r_scbond_it	4.755
r_mcangle_it	3.273
r_rigid_bond_restr	2.589
r_mcbond_it	2.073
r_angle_refined_deg	2.064
r_chiral_restr	0.154
r_bond_refined_d	0.03
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2427
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	8

Software

Software
Software Name	Purpose
DNA	data collection
SHELXS	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.